It would have interesting consequences on silver trade between Spanish Americas and China Sea (Manilla Galleons). Spaniards used Philippines as a doorway to this profitable trade OTL and without that, the most important contact with China to Europe would be Portuguese trade roads that wouldn't benefit from Spanish silver.
Now, I think that after some time, Spain would still search for a trade base in Far-East Asia and Phillipines would be a good choice, even if not the only one. So, I suppose their presence there is kind of hard to butterfly.
I doubt Japanese trade presence would eventually lead to a japenese takeover of the archipelago : they didn't really need a stronger presence, as they already had a part in China Sea trade and they didn't had the infrastructures to lead a massive trade between China Sea and Americas or elsewhere.